Payroll Onboarding

The article provides a comprehensive guide for completing the Payroll onboarding process in BambooHR. It outlines the purpose of the guide, emphasizing the importance of following the checklist to ensure readiness for working with a payroll project manager. The article includes a detailed table of contents covering various modules, such as Company Verification, Payroll Setup, and additional features. Each section contains specific tasks, including uploading necessary documents, verifying company information, setting up tax information, and completing training courses. The final steps involve account validation, approving payroll, notifying previous providers, and providing feedback. This structured approach aims to facilitate a smooth transition to BambooHR Payroll for users.

  • Apr 27, 2026
  • Knowledge

Title
Payroll Onboarding
Article Text
Payroll Onboarding is part of Payroll that is an add-on feature.

How do I complete the Payroll onboarding process?

Purpose: We understand you may need more direction when completing Payroll onboarding. This guide will walk you through each module and step within Payroll onboarding and direct you to where you can find more information for each task. Work through your entire checklist completely to lock in your implementation start date and to ensure your readiness to work with your payroll project manager.

If you have questions at any point during this process, please reach out to payrollimp@bamboohr.com.

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Table of Contents

Payroll Onboarding Overview

Whether you are a new customer starting onboarding from the beginning, or you have already onboarded with BambooHR and are adding Payroll, you will access your payroll modules from the Home tab after logging in. Click Start Implementation or Continue Implementation to begin. If you are a new customer, please click here to get familiar with the complete onboarding experience.

Every onboarding experience is tailored to the unique customer so what appears in your account may look different then what is outlined. If you have already onboarded with BambooHR, you will complete the Payroll and Company Verification modules. If it is your first time onboarding with BambooHR, there are important Payroll tasks throughout the Company Setup, Employee Data, and Benefits modules you will need to complete in addition to the Payroll module. If you have multiple EINs, you will see a Payroll Settings module for you to set up your additional EINs. Any additional data information that is required for a complete account setup can be found in the HR Implementation and Payroll Registration modules. This guide will explain the Payroll-specific modules of onboarding including:

  • Company Verification
  • Payroll
  • Payroll Setup

The other modules will have important payroll-related tasks as well. Click the links below to learn more:

Company Verification

The first step of the Company Verification onboarding module is the Intro section, with a video overview of the type of verification we need to process your payroll. Watch the video and continue to the second step, Upload Docs. This step is required before continuing with the other Payroll onboarding modules.

Upload Docs

We will need to verify your company’s legal name with what is on record with the IRS by uploading your Form 941 from the previous tax quarter. Click Choose File to select the appropriate file from their computer, and then click Upload. This will upload your file to the Payroll Implementation folder on the Files tab within BambooHR. If you are a new company or do not have Form 941, you can also upload the IRS CP 575/SS-4 return document.

Clicking Upload using Form 941 will automatically extract your company's EIN, federal deposit frequency, address, and company legal name for you to verify. You will also be required to add the company phone number and business type before saving the information. If you uploaded any other type of document, you will need to manually enter this information and verify that it is also correct.

Please note that the company's legal name registered with the state does not sync with the federal registration with the IRS. If any changes have occurred to your company's legal name with the state, and you did not file that change directly with the IRS, the federal legal name will remain the same until you update it with the IRS.

Need help verifying your tax frequency?

Your company will either be a monthly or a semi-weekly depositor. You can verify your federal tax deposit frequency schedule using your Form 941 or 944 filing documents. You can request a copy of your Form 941 or 944 from your previous payroll provider or the IRS.

If you are a new company, you will need to reach out to the IRS at 1 (800) 829-4933 or locate your deposit frequency using IRS Publication 15 (Section 11: Depositing Taxes) to determine your deposit schedule.

Please note that your deposit schedule is when you deposit your federal taxes and will not necessarily align with when you pay your employees.

Ownership

The last step is the Ownership section. You will first be prompted to select your company's business structure from the dropdown menu and then specify if your company falls within any of the specialized categories in the "Does your company fit any of these?*" dropdown.

You will then be prompted to select the type of ownership applicable to your company structure and provide the contact information of that person.

Click Next to continue and then confirm that all of the company information is correct. All fields marked with an asterisk are required.

A summary of your company structure and owner information will now display on the Ownership page. If you need to make and changes, click Contact Us to Change.

Payroll

Intro

Welcome to payroll in BambooHR! Before you get started on the Payroll onboarding module, feel free to watch this quick introduction video.

Heads up! BambooHR launched a newly refreshed UI, which means the product may appear differently in your account than what is shown in the video below. However, functionality will remain the same. Thank you for your patience as we continue to update our help content.

If you have multiple EINs (companies) that you are onboarding within a single BambooHR account, you can toggle between the EINs in the dropdown menu. You will need to complete the following steps for each EIN. Click Let's Go to move on to the next step.

You will receive email notifications throughout the process for tasks that are due and not yet complete or for tasks that are past due to help keep you on track. Click here for more information!

Company Taxes

The first task within the Company Taxes step is to complete a questionnaire. This survey helps us understand your company's unique payroll situation, such as the number of states your employees live in, additional pay types, 2% shareholders, and other details. This will help your future payroll project manager tailor your implementation to the specifics of your company as it currently stands, so answer the survey as best you can. Click Open Questionnaire to begin and click Done to mark the step task as complete.

After you have completed the questionnaire, you will begin working on entering your company tax information in Settings > Payroll. This help guide will be linked for your reference. Keep in mind the following:

Before we can begin to process and sync taxes in BambooHR Payroll, you will need to verify all of your tax information with your previous payroll provider by requesting a tax packet. The tax packet should include all tax IDs, rates, and frequencies (where applicable) for the states you are registered in. Once you have received the tax packet, you will need to upload the file to the Payroll Implementation folder on the Files tab in BambooHR. If you have not yet run payroll with any payroll provider, please request this information from your tax advisor.

Setting up company tax information in BambooHR

This information is vital in order to proceed with BambooHR Payroll.If you do not provide tax information (including state tax IDs) in a timely manner, it may result in the termination of services with BambooHR Payroll. This help guide may also assist you in finding your company tax information.

Click Set Up Taxes to navigate to the Taxes section of Settings > Payroll and complete the following:

  1. Confirm all demographic and payroll data is complete in BambooHR. All previous steps in your onboarding modules must be completed in order to proceed with syncing taxes in BambooHR Payroll. The best way to confirm that all employee data is complete is by using a few of our Missing Data reports in BambooHR.
    1. The Pay Info Tab Missing Data Report will show you any holes in your tax withholding and direct deposit information. This visual report shows red circles for missing data and green circles for completed data. If your report is empty, all employees have complete information for tax withholding and direct deposit!
    2. The Payroll Info Checkup Report will show you any Payroll-required fields that are missing for your employees. Simply select the syncing pay schedule to get started. This report will allow you to make updates directly from the report. If your report is empty, all employees have complete Payroll-related information!
  2. Verify data with your payroll project manager.
    1. Please allow 2-3 business days after you begin working directly with your payroll project manager to review your account and sync the remaining taxes.
  3. Once you have received confirmation from your payroll project manager that taxes have been synced, you can verify that all the taxes are correct in BambooHR by using the tax packet provided by your previous payroll provider.

For more information on how to manually add and set up your company tax information, click here.

Bank Authorization

After you submit your company bank documents (Form 8655, Beneficial Owner Addendum, and ACH Authorization) within the Company Setup module, our team will begin to process your application with the IRS and NPC. This process can take up to 10-15 business days from the time you submit your documents. Our team will notify you by email once the application process is complete and the penny test has been sent. After you view the email from our team, you can expect to see a small deposit and withdrawal—within two business days—in the bank account you have set up within this step. Enter that deposit amount in this step and click Verify to complete your penny verification task. Here is a helpful guide on the penny verification process.

If you have not completed you bank authorization forms in the Company Setup module, or we are waiting for NPC to process your application, the screen above will display.

Training

Within the Training step, you will complete two BambooHR Learning courses to ensure you understand how to run payroll like a pro with BambooHR Payroll:

  1. Payroll 101 - Preparing Your Account for Payroll
  2. Running a Payroll in BambooHR® - A Step-by-Step Guide

Click Done to complete the tasks and move to the next step.

Additional Features

There are four additional features included in BambooHR Payroll that may help you get the most out of your payroll experience: BambooHR Time & Attendance, Extra Pay, Payroll Reports, and Workers Comp. Not all of these features may apply to your unique company, but work through these tasks and see what else you can do to set yourself up for payroll success.

If you have hourly employees and Time & Attendance enabled in BambooHR, this step will guide you to Time & Attendance in Settings, where you can set up this feature. Remember, you can also add hours manually during the Run Payroll experience or import hours.

Extra pay can be handled differently across many companies, and BambooHR Payroll has made sure to cover all the bases. Click through the videos to learn about the different ways to add extra pay whether it is one-time extra pay or recurring.

Payroll reporting can be a powerful tool to help set you free to do other amazing things once you understand what data is available and how to use it. You will complete the Payroll Reporting in BambooHR learning course within this task.

Lastly, if your company operates in a state with workers' comp, this task will educate you on how to set that up in BambooHR and for your employees. Click the help guide within the task to learn more.

Final Steps

Within the Final Steps step, you will complete the following tasks:

  1. Account Validation Review
  2. Approve Payroll
  3. Notify Your Previous Payroll Provider
  4. Feedback Survey

Completing the account validation review will give you and our team peace of mind knowing your account is set up to process an accurate payroll. Review the checklist and confirm that your account setup looks ready to go. This part should be easy as our onboarding process has already led you to complete these items.

Drumroll please...the time has come! You are ready to approve your first payroll with BambooHR. Thank you for taking the time to clean your BambooHR account and running your first payroll! No one appreciates it more than your own employees, as it ensures they will be paid correctly and on time. If you have questions about what data is required for payroll, click here!

There is one more housekeeping item to ensure we cross our t's and dot our i's. You will need to notify your previous payroll provider that you are switching services so that they know not to process payroll. If two companies file on the same quarter or year-end, you can incur extra costs from the IRS. To avoid that, use the outlined email template to notify your previous payroll provider of the switch if you have not already done so.

Lastly, your feedback is of the utmost importance to us (behind helping you run an accurate and smooth payroll, of course). Click Open Feedback Survey to let us know how we did! Then click Done to complete the Payroll module!

Payroll Setup

Any miscellaneous items that are necessary for a complete and accurate payroll will live within the Payroll Setup Module. This module includes the following steps:

Payroll Contact 

In the Payroll Contact task, you will select the primary contact for the Payroll onboarding experience by choosing from the Account Owner or Full Admin(s) in the drop-down menu. Payroll admins are not included. If you add a new user, they will have Full Admin access to BambooHR.

The Payroll contact will also have access to the related EIN once the Form 941 is uploaded. If the Payroll contact is later changed, you will need to confirm whether the previous Payroll contact will retain access to the EIN or if they should be removed. Either way, they will still have Full Admin access to BambooHR.

Payroll Agreement 

This task allows you to check the box indicating your acceptance of our Payroll Services Agreement. Clicking View Payroll Services Agreement opens the agreement for your review. The Next button is disabled until you mark the checkbox indicating your acceptance of the agreement.

Bank

It is important to enter this information as soon as possible so that we may continue with your onboarding. If needed, you can work with BambooHR to change the bank information later in the process.

Bank account information is vital for your application to our bank, NPC (National Payment Corporation). Click Connect via Plaid to open Plaid and find your bank. BambooHR uses Plaid to verify your bank account securely. Once filled out, the bank account information will automatically populate on your ACH Authorization document.

If you are having difficulty entering your bank account when using Plaid, there is an option to enter your account information manually by clicking Add Bank Manually. Please ensure you enter your information correctly so we do not run into any issues with NPC or the next steps. This help guide walks you through exactly how to add your account manually.

Sign Docs

Click Download 4 documents. There are four onboarding documents you are required to download, complete, and sign for our team to begin processing forms with the IRS and NPC:

  • IRS Form 8821
  • IRS Form 8655
  • ACH Authorization
  • Beneficial Owner(s) Addendum

These documents must be filled out using a 'wet' signature (see requirements below)*. If you need help, check out this help guide that walks you through each step and gives examples of what your documents should look like.

*Signature requirements

Keep in mind that an authorized individual of your company (Owner, CEO, President, etc.—please see the image below for accepted titles) must sign each of the IRS forms using a physical "wet" signature.

Pay Schedules

Would you like to review a step-by-step help guide on how to set up pay schedules in BambooHR?

You must set up your pay schedules, assign your employees to the pay schedule, and ensure the pay schedule is syncing to Payroll. Pay schedules are the linking factor between BambooHR and Payroll and must have the correct pay period dates and pay dates. This step will walk you through how to set up a pay schedule in your account. Click + New Pay Schedule to begin.

Enter your pay schedule details in Step 1, including the Pay Schedule Name, Frequency, Pay Period end dates, Pay Days, and rules for weekends/holidays.

A calendar on the right updates in real-time to visualize the pay periods and pay dates based on the user's selections.For less common frequencies (Quarterly, Yearly, etc.), the preview displays as a timeline instead of a calendar.

Click Next to continue to Step 2 of your pay schedule setup.

After completing the schedule details, specify you need to include the pay schedule in BambooHR Payroll.

If you select, "Yes, include them in Payroll", you must define the "First Pay Period" to run with BambooHR and the standard "Hours per week" for salaried employees on this schedule.

Click Finish to complete the setup.

You can manually assign the pay schedule to an employee in the Compensation table on their Job tab. This is a great opportunity to verify that other data, such as the Overtime Status and Paid Per* fields, have been entered correctly on the employee’s profile.

*The only options that will sync to Payroll from the Compensation table’s Paid Per field are paid per Hour or paid per Year.

Tips for setting up syncing pay schedules
  1. You can assign employees to a pay schedule after it has been synced. However, all required Personal and Job tab information must be added to the employee profile before assigning the pay schedule. We recommend creating the pay schedule without syncing it to Payroll, verifying the pay dates, assigning your employees, and then going back and editing the pay schedule to sync to Payroll.
  2. If you have employees with the same pay period start, end, and pay dates, but some get paid through Payroll while some do not, you will need to create two identical pay schedules with different names and mark one as syncing to Payroll while leaving the other as unsynced.
  3. You will not be able to edit the pay period and pay date after you add the syncing pay schedule, so please ensure that the pay schedule and pay dates are accurate. If the dates are wrong after it is saved, you will have to create a new pay schedule and reassign your employees.
  4. After creating your pay schedule, verify that the pay periods and pay dates look correct by hovering over the pay schedule and clicking on the calendar icon. This will bring up a window that shows the pay schedule start, end, and pay dates.
Tax Questionnaire

Help us understand the type of business you run and how it is taxed so we can ensure your account is set up to be filed correctly.

Tax Docs

We will also request the appropriate tax documents from your company for payroll processing. To ensure we collect the correct documents, you will need to answer the following two questions:

  1. “Has [Your Company Name associated with this EIN] paid employees before?”
  2. “Does your business use a PEO (Professional Employer Organization)?”

The system will then prompt you to upload either your tax returns or additional state tax documents. To save and upload your files, click Upload. You can find all uploaded files in the Payroll Implementation folder on the Files tab.

Payroll History

Now that you have all of your settings and employee data complete, it is time to provide some important payroll data from your previous payroll provider. We will need to obtain a year-to-date (YTD) and/or quarter-to-date (QTD) file with all wages, taxes, and deduction information from all active and terminated employees within the current year and/or quarter so that we can create your end-of-year tax documents. Depending on the time of year when you run your first payroll with BambooHR, the lookback period of data we need to collect will be determined. Watch this short video to understand which YTD/QTD files are the most helpful.

You will then need to select the name of your previous payroll provider and use this help guide to help you identify which report we need from you.

Uploading the correct YTD reports
  • This is not applicable to new companies (never paid employees before) or if it's your company's first pay date in the new year.
  • We will need a year-to-date report (YTD) of all the payroll runs made by your previous payroll provider from the beginning of the year (including any off-cycle checks). If you are unsure of which dates we will need for your reports, refer to the date range we provided below the Previous Provider Name field. This date range is based on your first pay date, so make sure it is accurate. It is very important that your report reflects the accurate dates so that we can ensure every wage, tax, and deduction is accounted for when creating your employees’ W-2s at the end of the year. Your report(s) should show the totals of all wage, deduction, and tax information for every employee paid during the year. Once the correct YTD information has been identified and the reports have been run, you can then upload this report within this step by clicking Choose Files.

Upload Quarter-to-Date Data

If you are starting with BambooHR Payroll mid-quarter, you must upload a quarter-to-date (QTD) report in addition to the YTD report you previously uploaded within the Previous Provider Data step. Click the Previous Provider Name dropdown and choose + Add Provider to select your previous payroll provider. If you are unsure which dates we will need for this report, refer to the date range we provide. You can also reach out to your PPM for confirmation. It is very important that your reports reflect the accurate dates so that we can ensure every wage, tax, and deduction is accounted for when creating your employees’ W-2s at the end of the year. Your report(s) should show the totals of all wage, deduction, and tax information for every employee paid during the quarter. Once the correct QTD information has been identified and the reports have been run, you can upload this report by clicking Choose Files. The system will automatically mark this step as complete once you upload your file.

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